How to close only one window of an application?

Probably the easiest option is using wmctrl -c. You might have to install it first:

~$ sudo apt-get install wmctrl

then to close a window named "example" (no matter what application it belongs to), use the command:

~$ wmctrl -c "example"

More options

However, there are many more options to close a specific window, depending on your "angle of incidence".

A few examples:

1. To close a specific window by clicking on it:

   ~$ wmctrl -c :SELECT:
   [then click on the window to be closed]
   

2. To close a specific window by its numeric id:

   ~$ wmctrl -ic <numeric_id>
   

3. To close the active window:

   ~$ wmctrl -c :ACTIVE:
   

4. To use the pid to get a list of windows, owned by a specific application (e.g. gedit):

   ~$ pidof gedit
   22576
   
   ~$ wmctrl -l -p | grep 22576
   0x04600085  0 22576  jacob-System-Product-Name get.sh (~/Bureaublad) - gedit
   0x0461aee4  0 22576  jacob-System-Product-Name verhaal (~/Bureaublad) - gedit
   0x0461b0a1  0 22576  jacob-System-Product-Name *Niet-opgeslagen document 1 - gedit
   

   then close the specific window get.sh by either:

   wmctrl -c get.sh
   

   or:

   wmctrl -ic 0x04600085
   

5. If you know only part of the window name, e.g. there is a window; monkey eats banana.txt, you know it has banana in its name,

   • first bring the window to front:

     wmctrl -a banana
     

   • then decide if you want to close the window (as active window for example)

options are numerous, see also man wmctrl. man wmctrl